Metal binding affinity and selectivity in metalloproteins: Insights from computational studies

Annual Review of Biophysics

Volumn 37, Issue , 2008, Pages 97-116

  Dudev, Todor ^a   Lim, Carmay ^a  

^a INSTITUTE OF BIOMEDICAL SCIENCES   (Taiwan)

Author keywords

Binuclear enzymes; Metal binding residues; Protein aggregation; Protein flexibility; Protein metal recognition; Proton transfer

Indexed keywords

ASPARTIC ACID; GLUTAMIC ACID; METAL ION; METALLOPROTEIN; SOLVENT; WATER; ALUMINUM; ANION; CALCIUM ION; LANTHANIDE; LIGAND; MAGNESIUM ION; MERCURY; ZINC ION; METAL;

ALGORITHM; BINDING AFFINITY; LIGAND BINDING; METAL BINDING; MOLECULAR RECOGNITION; NONHUMAN; PRIORITY JOURNAL; PROTEIN AGGREGATION; PROTEIN BINDING; PROTEIN STRUCTURE; PROTEIN TRANSPORT; REVIEW; BINDING SITE; ENERGY TRANSFER; HYDROGEN BOND; MATHEMATICAL MODEL; PROTEIN SECONDARY STRUCTURE; PROTON TRANSPORT; CHEMICAL MODEL; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER SIMULATION; PROTEIN CONFORMATION; ULTRASTRUCTURE;

BINDING SITES; COMPUTER SIMULATION; METALLOPROTEINS; METALS; MODELS, CHEMICAL; MODELS, MOLECULAR; PROTEIN BINDING; PROTEIN CONFORMATION;

EID: 48249153490     PISSN: 1936122X     EISSN: None     Source Type: Book Series    
DOI: 10.1146/annurev.biophys.37.032807.125811     Document Type: Review

References (61)

1. Akabas MH. 2001. Chloride channels. In Encyclopedia of Life Sciences, pp. 1-7. London: Macmillan Reference Ltd.
2. Babu CS, Dudev T, Casareno R, Cowan JA, Lim C. 2003. A combined experimental and theoretical study of divalent metal ion selectivity and function in proteins: application to E. coli ribonuclease H1. J. Am. Chem. Soc. 125:9318-28
3. Bertini I, Sigel A, Sigel H, eds. 2001. Handbook on Metalloproteins. New York: Marcel Dekker
4. Bracken C, Iakoucheva LM, Romero PR, Dunker AK. 2004. Combining prediction, computation and experiment for the characterization of protein disorder. Curr. Opin. Struct. Biol. 14:570-76
5. Christianson DW, Cox JD. 1999. Catalysis by metal-activated hydroxide in zinc and manganese metalloenzymes. Annu. Rev. Biochem. 68:33-57
6. Collery P, Pirer L, Manfait M, Etienne JE. 1990. Alzheimer's Disease and Dementia Syndromes Consecutive to Imbalanced Mineral Metabolisms Subsequent to Blood Brain Barrier Alteration. London-Paris: John Libbey-Eurotext
7. Cui Q, Karplus M. 2003. Is a "proton wire" concerted or stepwise? A model study of proton transfer in carbonic anhydrase. J. Phys. Chem. B 107:1071-78
8. Decorrnez H, Drukker K, Hammes-Schiffer S. 1999. Solvation and hydrogen-bonding effects in proton wires. J. Phys. Chem. A 103:2891-98
9. 2+ binding-induced destabilization of β2-microglobulin revealed by molecular dynamics simulation. Biophys. J. 90:3865-79
10. Dismukes GC. 1996. Manganese enzymes with binuclear active sites. Chem. Rev. 96:2909-26
11. Dodgson SJ, Tashian RE, Gross G, Carter ND. 1991. The Carbonic Anbydrases. New York: Plenum
12. 2+ in metalloproteins: a DFT/CDM study. J. Am. Chem. Soc. 127:4091-103
13. Dudev T, Cowan JA, Lim C. 1999. Competitive binding in magnesium coordination chemistry: water versus ligands of biological interest. J. Am. Chem. Soc. 121:7665-73
14. 2+. J. Phys. Chem. B 105:4446-52
15. Dudev T, Lim C. 2003. Metal binding and selectivity in zinc proteins. J. Chin. Chem. Soc. 50:1093-102
16. Dudev T, Lim C. 2003. Principles governing Mg, Ca, and Zn binding and selectivity in proteins. Chem. Rev. 103:773-87
17. Dudev T, Lim C. 2006. A DFT/CDM study of metal-carboxylate interactions in metalloproteins: factors governing the maximum number of metal-bound carboxylates. J. Am. Chem. Soc. 128:1553-61
18. Dudev T, Lim C. 2006. Competition between protein ligands and cytoplasmic inorganic anions for the metal cation: a DFT/CDM study. J. Am. Chem. Soc. 128:10541-48
19. Dudev T, Lim C. 2007. Effect of carboxylate-binding mode on metal binding/selectivity and function in proteins. Acc. Chem. Res. 40:85-93
20. Dudev T, Lin YL, Dudev M, Lim C. 2003. First-second shell interactions in metal-binding sites in proteins: a PDB survey and DFT/CDM calculations. J. Am. Chem. Soc. 125:3168-80
21. n. J. Phys. Chem. 74:1466-74
22. Falke JJ, Drake SK, Hazard AL, Peersen OB. 1994. Molecular tuning of ion binding to calcium signaling proteins. Q. Rev. Biophys. 27:219-90
23. Floege J, Ehlerding G. 1996. β2-microglobulin-associated amyloidosis. Nephron 72:9-26
24. Frausto da Silva JJR, Williams RJP. 1991. The Biological Chemistry of the Elements. Oxford: Oxford Univ. Press
25. Garmer DR, Gresh N. 1994. A comprehensive energy component analysis of the interaction of hard and soft dications with biological ligands. J. Am. Chem. Soc. 116:3556-67
26. Gerstein M, Echols N. 2004. Exploring the range of protein flexibility from a structural proteomics perspective. Curr. Opin. Chem. Biol. 8:14-19
27. n clusters for alkali metals, M = Li, Na, K, Rb and Cs. J. Phys. Chem. 99:3060-67
28. 2+ to biologically relevant ligands: combined ab initio SCF supermolecule and molecular mechanics investigation. J. Comp. Chem. 17:1481-95
29. Hartley BS, Hanlon N, Jackson RJ, Rangarajan M. 2000. Glucose isomerase: insights into protein engineering for increased thermostability. Biochim. Biophys. Acta 1543:294-335
30. Katz AK, Glusker JP, Beebe SA, Bock CW. 1996. Calcium ion coordination: a comparison with that of Be, Mg and Zn. J. Am. Chem. Soc. 118:5752-63
31. 2+ binding to calmodulin loop. Biophys. J. 90:3043-51
32. 2+ interactions with peptides and aminoglycosides. Coord. Chem. Rev. 249:2323-34
33. Krebs JF, Rana F, Dluhy RA, Fierke CA. 1993. Kinetic and spectroscopic studies of hydrophilic amino-acid substitutions in the hydrophobic pocket of human carbonic anhydrase II. Biochemistry 32:4496-505
34. Lai W-L, Chou L-Y, Ting C-Y, Kirby R, Tsai Y-C, et al. 2004. The functional role of the binuclear metal center in D-aminoacylase. J. Biol. Chem. 279:13962-67
35. Lin H, Truhlar DG. 2007. QM/MM: What have we learned, where are we, and where do we go from here? Theor. Chem. Acc. 117:185-99
36. Lin Y-L, Lee Y-M, Lim C. 2005. Differential effects of the Zn-His-Bkb vs Zn-His-[Asp/Glu] triad on Zn-core stability and reactivity. J. Am. Chem. Soc. 127:11336-47
37. Lin Y-L, Lim C. 2004. Factors governing the protonation state of Zn-bound histidine in proteins: a DFT/CDM study. J. Am. Chem. Soc. 126:2602-12
38. Lindskog S. 1997. Structure and mechanism of carbonic anhydrase. Pharmacol. Ther. 74:1-20
39. Lippard SJ, Berg JM. 1994. Principles of Bioinorganic Chemistry. Mill Valley, CA: Univ. Science Books
40. Lovell T, Himo F, Han W-G, Noodleman L. 2003. Density functional methods applied to metalloenzymes. Coord. Chem. Rev. 238-239:211-32
41. Lu DS, Voth GA. 1998. Proton transfer in the enzyme carbonic anhydrase: an ab initio study. J. Am. Chem. Soc. 120:4006-14
42. MacDonald TL, Martin RB. 1988. Aluminium ion in biological systems. Trends Biochem. Sci. 13:15-19
43. Mercero JM, Matxain JM, Rezabal E, Lopez X, Ugalde JM. 2004. The first solvation shell of aluminium(III) and magnesium(II) cations in a protein model environment. Int. J. Quant. Chem. 98:409-24
44. Pavlov M, Siegbahn PEM, Sandström M. 1998. Hydration of beryllium, magnesium, calcium and zinc ions using density functional theory. J. Phys. Chem. A 102:219-28
45. Pierce BS, Hendrich MP. 2005. Local and global effects of metal binding within the small subunit of ribonucleotide reductase. J. Am. Chem. Soc. 127:3613-23
46. + conduction along hydrogen-bonded chains of water molecules. Biophys. J. 75:33-40
47. +] interactions with the aromatic motifs of naturally occurring amino acids: a theoretical study. J. Phys. Chem. A 109:8893-903
48. Rezabal E, Mercero JM, Lopez X, Ugalde JM. 2006. A study of the coordination shell of aluminium(III) and magnesium(II) in model protein environments: thermodynamics of the complex formation and metal exchange reactions. J. Inorg. Biochem. 100:374-84
49. Rosso KM, Rustad JR, Gibbs GV. 2002. Trivalent ion hydrolysis reactions II: analysis of electron density distributions in metal-oxygen bonds. J. Phys. Chem. A 106:8133-38
50. Rulisek L, Havlas Z. 2003. Theoretical studies of metal ion selectivity. 3. A theoretical design of the most specific combinations of functional groups representing amino acid side chains for the selected metal ions. J. Phys. Chem. B 107:2376-85
51. Schachtman DP, Reid RJ, Ayling SM. 1998. Phosphorus uptake by plants: from soil to cell. Plant. Physiol. 116:447-53
52. Schmitt UW, Voth GA. 1999. The computer simulation of proton transport in water. J Chem. Phys. 111:9361-81
53. 4 complexes of group 11 cations: periodic trends and relativistic effects in the involvement of (n-1)d, ns, and np orbitals in the metal-ligand interactions. Organometallics 23:2343-49
54. Tai H-C, Lim C. 2006. Computational studies of the coordination stereochemistry, bonding, and metal selectivity of mercury. J. Phys. Chem. A 110:452-62
55. Toba S, Colombo G, Merz KM. 1999. Solvent dynamics and mechanism of proton transfer in human carbonic anhydrase II. J. Am. Chem. Soc. 121:2290-302
56. Tunell I, Lim C. 2006. Factors governing the metal coordination number in group IA and IIA metal hydrates. Inorg. Chem. 45:4811-19
57. Wang W, Donini O, Reyes CM, Kollman PA. 2001. Biomolecular simulations: recent developments in force fields, simulations of enzyme catalysis, protein-ligand, protein-protein, and protein-nucleic acid noncovalent interactions. Annu. Rev. Biophys. Biomol. Struct. 30:211-43
58. Warshel A. 2002. Molecular dynamics simulations of biological reactions. Acc. Chem. Res. 35:385-95
59. Williams RJP. 1997. The natural selection of the chemical elements. Cell. Mol. Life Sci. 53:816-29
60. Wilson CJ, Apiyo D, Wittung-Stafshede P. 2004. Role of cofactors in metalloprotein folding. Q. Rev. Biophys. 37:285-314
61. Yang T-Y, Dudev T, Lim C. 2008. Mononuclear versus binuclear metal-binding sites: metal-binding affinity and selectivity from PDB survey and DFT/CDM calculations. J. Am. Chem. Soc. [Epub ahead of print]